Strain identifier

BacDive ID: 6263

Type strain: Yes

Species: Janibacter melonis

Strain Designation: CM2104

Strain history: CIP <- 2005, JCM <- J. H. Yoon: strain CM2104

NCBI tax ID(s): 1216971 (strain), 262209 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6249

BacDive-ID: 6263

DSM-Number: 16063

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Janibacter melonis CM2104 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from oriental melon.

NCBI tax id

NCBI tax idMatching level
262209species
1216971strain

strain history

@refhistory
6249<- J.-H. Yoon; CM2104
67770J.-H. Yoon CM2104.
67771<- JH Yoon, KRIBB
120887CIP <- 2005, JCM <- J. H. Yoon: strain CM2104

doi: 10.13145/bacdive6263.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Janibacter
  • species: Janibacter melonis
  • full scientific name: Janibacter melonis Yoon et al. 2004

@ref: 6249

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Janibacter

species: Janibacter melonis

full scientific name: Janibacter melonis Yoon et al. 2004

strain designation: CM2104

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31267positive0.9 µm0.9 µmcoccus-shapedno
67771positive
120887positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19739Ivory (1014)10-14 daysISP 2
19739Ivory (1014)10-14 daysISP 3
19739Ivory (1014)10-14 daysISP 4
19739Ivory (1014)10-14 daysISP 5
19739Ivory (1014)10-14 daysISP 6
19739Ivory (1014)10-14 daysISP 7
602162 days
120887

multicellular morphology

@refforms multicellular complexmedium name
19739noISP 2
19739noISP 3
19739noISP 4
19739noISP 5
19739noISP 6
19739noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6249RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
6249TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
19739ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19739ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19739ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19739ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19739ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19739ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40492MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120887CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112
120887CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19739positiveoptimum28mesophilic
6249positivegrowth28mesophilic
31267positivegrowth10-40
31267positiveoptimum30mesophilic
40492positivegrowth30mesophilic
60216positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
120887positivegrowth15-37
120887nogrowth10psychrophilic
120887nogrowth41thermophilic
120887nogrowth45thermophilic

culture pH

@refabilitytypepH
31267positivegrowth5.5-7
31267positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31267aerobe
60216aerobe
67771aerobe
120887obligate aerobe

spore formation

  • @ref: 31267
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31267NaClpositivegrowth02-06 %
31267NaClpositiveoptimum4 %
120887NaClpositivegrowth0-4 %
120887NaClnogrowth6 %
120887NaClnogrowth8 %
120887NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1973962968cellulose+
1973916634raffinose-
1973926546rhamnose-
1973928757fructose+
1973929864mannitol+
1973917268myo-inositol+
1973918222xylose-
1973917992sucrose+
1973922599arabinose-
1973917234glucose+
3126730089acetate+carbon source
3126716947citrate+carbon source
3126715740formate+carbon source
3126725115malate+carbon source
312674853esculin+hydrolysis
3126717632nitrate+reduction
12088716947citrate+carbon source
1208874853esculin+hydrolysis
120887606565hippurate+hydrolysis
12088717632nitrate+reduction
12088716301nitrite-reduction
12088717632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

antibiotic resistance

  • @ref: 120887
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120887
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12088715688acetoin-
12088717234glucose-

enzymes

@refvalueactivityec
31267catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
120887oxidase-
120887beta-galactosidase+3.2.1.23
120887alcohol dehydrogenase-1.1.1.1
120887gelatinase+
120887amylase+
120887DNase+
120887caseinase-3.4.21.50
120887catalase+1.11.1.6
120887tween esterase+
120887gamma-glutamyltransferase+2.3.2.2
120887lecithinase-
120887lipase-
120887lysine decarboxylase-4.1.1.18
120887ornithine decarboxylase-4.1.1.17
120887phenylalanine ammonia-lyase-4.3.1.24
120887tryptophan deaminase-
120887urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19739-----+-++-+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19739-+++++-+------++---
120887+++-+--+-+----++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120887++++++-+-+++++++++-+++---+++-+--++++-+---+-+-+--+-++-++-----+-----+--++-+++-------+------++++-+++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost species
6249oriental melonRepublic of KoreaKORAsia
60216Melon,abnormally spoiled oriental melonRepublic of KoreaKORAsia
67770Abnormally spoiled oriental melon (Cucumis melo)Republic of KoreaKORAsiaCucumis melo
67771From MelonRepublic of KoreaKORAsia
120887Food, Abnormally spoiled oriental melon (Cucumis melo)Republic of KoreaKORAsia

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Plant
  • Cat3: #Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8290.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_927;97_1079;98_6034;99_8290&stattab=map
  • Last taxonomy: Janibacter melonis subclade
  • 16S sequence: AY522568
  • Sequence Identity:
  • Total samples: 1228
  • soil counts: 27
  • aquatic counts: 41
  • animal counts: 1135
  • plant counts: 25

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62491Risk group (German classification)
197391Risk group (German classification)
1208871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Janibacter melonis DNA, 16S-23S rRNA spacer region sequenceAB292735402ena262209
31267Janibacter melonis strain CM2104 16S ribosomal RNA gene, partial sequenceAY5225681479nuccore262209

Genome sequences

  • @ref: 66792
  • description: Janibacter melonis NBRC107855
  • accession: GCA_020567375
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 262209

GC content

@refGC-contentmethod
3126773
6777073high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.016yes
gram-positiveyes92.469no
anaerobicno98.324yes
aerobicyes92.469yes
halophileno95.307no
spore-formingno90.245yes
motileno95.135yes
thermophileno98.692no
glucose-utilyes92.444no
glucose-fermentno89.26no

External links

@ref: 6249

culture collection no.: CCUG 54528, CIP 108643, DSM 16063, JCM 12321, KCTC 9987, NBRC 107855

straininfo link

  • @ref: 75740
  • straininfo: 134427

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545420Janibacter melonis sp. nov., isolated from abnormally spoiled oriental melon in Korea.Yoon JH, Lee HB, Yeo SH, Choi JEInt J Syst Evol Microbiol10.1099/ijs.0.63167-02004Actinomycetales/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cucurbitaceae/*microbiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Diaminopimelic Acid/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Peptidoglycan/chemistry, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis/isolation & purificationEnzymology
Genetics21075932Genome sequence of the Marine Janibacter Sp. Strain HTCC2649.Thrash JC, Cho JC, Bertagnolli AD, Ferriera S, Johnson J, Vergin KL, Giovannoni SJJ Bacteriol10.1128/JB.01298-102010Actinomycetales/*genetics/isolation & purification, Bermuda, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Molecular Sequence Data, Sequence Analysis, DNA, Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6249Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16063)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16063
19739Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16063.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31267Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127587
40492Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6294
60216Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54528)https://www.ccug.se/strain?id=54528
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75740Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134427.1StrainInfo: A central database for resolving microbial strain identifiers
120887Curators of the CIPCollection of Institut Pasteur (CIP 108643)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108643